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Philipp-Neubauer / PopR

Analysis of population structure in R using finite and infinite Bayesian mixture models
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DPM.call.R returns errors #1

Open dretreml opened 11 years ago

dretreml commented 11 years ago

I'm using PopR downloaded on 7July2013 with Julia 0.1.2 downloaded on 19July2013 (julia0.1.2-WINNT-i686+Git.zip) from Rstudio running R (R-2.15.2) on a Windows7 64bit machine. I've updated Julia and confirm that Julia works fine at the command line. Running 'test-julia.bat' returns one error from the unicode test, all other tests pass.

In using 'Toy data creator.R' (https://github.com/Philipp-Neubauer/PopR/blob/master/Toy%20data%20creator.R), DPM.call.R (line 1111) starts Julia, but never returns to R. After killing the Julia process, the following errors are returned:

Warning messages: 1: running command '"C:/etreml/REEF/Otolith//julia/julia.bat" -p 3 C:/Users/Eric Treml/Documents/R/win- library/2.15/PopR/exec/call_DPM.jl 0 1000 1 N C:/etreml/REEF/Otolith/analysis' had status 24 2: In file(file, "rt") : cannot open file 'source_ids.csv': No such file or directory

Further diagnostics reveal that directory strings may be formatted incorrectly and/or pointing to the wrong places and/or something related to 'ErrorException("syntax: expected identifier after const")'. Assistance in getting past this would be much appreciated.

Philipp-Neubauer commented 11 years ago

Ok, finally got this sort - or so I think.

there were a number of issues:

  1. you need to run julia 0.2.0 as some of the functions don't exist, or under different names in 0.1.x
  2. there were some issues with recent julia builds that caused memory leaks in parallel computations. I switched to just local computations for now. Please use the new files on sourceforge, or, when building from the github source, use the temp branch for now
  3. when julia is installed, call julia just once to install the 'Distributions' package with Pkg.add("Distributions")
Philipp-Neubauer commented 11 years ago

Actually, there still seems to be an odd end-of-line problem under windows. Will look into it asap

Thom4sR commented 10 years ago

Hi, This issue happens also with recent versions of julia, I had this with julia 0.2.1 and now with julia 0.3.2, thus I never managed to run the code here is the error I get: Error in file(file, "rt") : cannot open the connection In addition: Warning messages: 1: running command '"F://julia/julia.bat" -p 1 C:/Users/regniert/Documents/R/win-library/3.1/PopR/exec/call_DPM.jl 0 1000 1 N C:/Users/regniert/Documents C:/Users/regniert/Documents/R/win-library/3.1/PopR/exec' had status 127 2: In file(file, "rt") : cannot open file 'source_ids.csv': No such file or directory

I provided the path to julia, even the one to popR exec but after many attempts, I did not manage, thus I have no prior knowledge of julia... If any one can help?

Best regards

Thomas

Philipp-Neubauer commented 10 years ago

Cheers Thomas, I believe I had this resolved but must have failed to post the fix here; I'll go back through my email to check. I might try on my windows PC too, if I can manage to get it to run (it hasn't been fired up for months, so no guarantees at this point ;)

Philipp-Neubauer commented 10 years ago

Ok, it doesn't look like it got fixed, rather researchers who reported back with issues ran it on mac (or ended up doing so). A few suggestions:

I don't expect it to work with Julia 0.3.x since I haven't updated to code and Julia is very actively developed. I will do so at some point, but it's a never ending battle to keep up (especially on all platforms), and the more sensible option at this point would be to distribute the package in a Docker environment with Rocker, to make sure it works straight out the box. For now going with Julia 0.2.1 should be a safer bet.

The problem as stated above doesn't seem to be julia related - i.e., Julia doesn't seem to be throwing an error. Does the double slash after the drive letter mess things up? Not sure if the windows shell can cope with that (it seems like it caused an issue before...).

hope this helps

Thom4sR commented 10 years ago

I am running it with version 0.2.1 and indeed problems seems to come from double slash.

sorry for that

Best

Thomas

Philipp-Neubauer commented 10 years ago

great, does that mean that it actually runs now?

On Tue, Nov 11, 2014 at 3:43 AM, Thom4sR notifications@github.com wrote:

I am running it with version 0.2.1 and indeed problems seems to come from double slash.

sorry for that

Best

Thomas

— Reply to this email directly or view it on GitHub https://github.com/Philipp-Neubauer/PopR/issues/1#issuecomment-62392889.

Phil